compare: Compare two codelists
In CALIBERcodelists: Generate ICD10, Read and OPCS codelists

Description Usage Arguments Details Value Note See Also Examples

Compares one codelist against another, or compares a codelist against the selection in the master dictionary. Returns a list of differences and a set of instructions for updating the master dictionary from the older codelist to the newer one.

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compare(oldlist, newlist = NULL, expandICD10 = TRUE, expandICD9 = TRUE)
## S3 method for class 'codelistComparison'
print(x, ...)

`oldlist`	The first codelist for the comparison, ideally the older codelist. If the master dictionary is to be considered as `oldlist`, it can be supplied as the argument by coercing it to a codelist using e.g. `oldlist = as.codelist('read')` (replacing 'read' by 'icd10' or 'opcs' as appropriate).
`newlist`	The second codelist to compare against, or NULL to compare against the master dictionary.
`expandICD10`	TRUE or FALSE, whether to ensure that ICD-10 codelists are in the 'Expanded' form before doing the comparison. The codelists should both be in the same form before comparison, and the expanded form might give a more informative comparison. See `expandCodelist`.
`expandICD9`	TRUE or FALSE, whether to ensure that ICD-9 codelists are in the 'Expanded' form before doing the comparison.
`x`	a `codelistComparison` object as returned by the `compare` function.
`...`	not used

Missing categories and categories less than one are lumped together as 'Excluded' terms for the purposes of comparison.

A list object of class codelistComparison, with the following elements:

`same_terms`	whether all the terms are the same (considering terms with category 0 and missing terms as equivalent)
`same_attr`	whether all the attributes are the same
`same_cattable`	whether all the category descriptions are the same
`cattable_comparison`	data.table comparing category tables
`attr_comparison`	data.table comparing attributes
`terms_comparison`	data.table comparing old and new terms
`message`	Comparison of terms, as reported by the `print` method
`instructions`	R code for updating the master dictionary from oldlist to newlist
`identical`	TRUE or FALSE according to whether the categories (ignoring 0), category descriptions and other attributes are identical between the two codelists.

The instructions can be parsed and evaluated by assigncat to convert the selection of terms in the master dictionary from oldlist to newlist.

as.codelist, assigncat, contractCodelist, expandCodelist, is.codelist, print.codelist, subset.codelist

setdictionary('read')
# Generate codelists
c1 <- as.codelist(termhas('angina|myocardial infarct'))
c2 <- as.codelist(termhas('myocard'))

# Generate a codelist with a category
assigncat(1, 'myocard', termhas('myocard'))
c3 <- as.codelist()

# Compare codelists
compare(c1, c3)
compare(c1, c2)
# Codelists c1 and c2 have no category assigned so they cannot be compared

# Use the data.table function to set a category for both codelists
# 1L means the number 1 as an integer rather than the real number 1.0000 ...
# This is to avoid a data.table warning, although c1[, category:=1] would also
# work. You can update a subset of categories like this:
# c1[readcode %like% '^12C', category:=2L]
c1[, category:=1L]
c2[, category:=1L]

# Now compare them again
compare(c1, c2)
compare(c2, c1)
compare(c1, c2)$identical